Micrroarray biochips are being increasingly used for the performance of large numbers of closely related chemical tests. For example, to ascertain the genetic differences between lung tumors and normal lung tissue one might deposit small samples of different cDNA sequences under a microscope slide and chemically bond them to the glass. ten thousand or more such samples can easily be arrayed as dots on a single microscope slide using mechanical microarraying techniques. Next, sample mRNA is extracted from normal lung tissue and from a lung tumor. The mRNA represents all of the genes expressed in these tissues and the differences in the expression of mRNA between the diseased tissue and the normal tissue can provide insights into the cause of the cancer and perhaps point to possible therapeutic agents as well. The "probe"samples from the two tissues are labeled with different fluorescent dyes. A predetermined amount of each of the two samples is then deposited on each of the microarray dots where they competitively react with the cDNA molecules. The mRNA molecules that correspond to the cDNA strands in the array dots bind to the strands and those that do not are washed away.
The slide is subsequently processed in a scanner that illuminates each of the dots with laser beams whose wavelengths correspond to the fluorescences of the labeling dyes, The fluorescent emissions are sensed and their intensity measured to ascertain for each of the array dots the degree to which the mRNA samples correspond to the respective cDNA sequences. In the experiment outlined above the image scanner separately senses the two fluorescences and thereby provides separate maps of the reactions of the mRNA extracted from the normal and tumorous tissues. The scanner generates an image map of the array, one for each of the fluorescenses. The maps are ultimately analyzed to provide meaningful information to the experimenter.
Microarray biochips are available in a variety of form factors and they may contain one or more different fluorescence labels. The reagents involved in the chemical reactions in the array dots are typically biological samples such as DNA, RNA, peptides, proteins or other organic molecules. The biochips might be used for diagnostics, screening assays, genetics and molecular biology research. They may include, in addition to the test dots, carlibration dots containing known amounts of the fluorescent materials. Scanning of the latter dots thus serves to calibrate the readings obtained from the test dots.
In order to obtain accurate information from the scanning of a biochip array, it is important to know which fluorescence materials have been used, in where the array is located, and the locations of the calibration dots, if any. It is important to know the fluorescent materials in order to use the correct wavelengths in illuminating the dots and to filter the correct wavelengths of the fluorescent omissions. Furthermore, it is advantageous to excite the fluorescenses with a high intensity so as to provide the maximum signal to the fluorescence detector. However, the intensity must be kept below the level at which the flurorescense is saturated or the fluorescent material is degraded and this depends on the particular fluorescent material that is used.
Furthermore, analysis of raw data collected by the scanner must be performed in accordance with protocols that may vary in accordance with experiment parameters. Prior to the present invention entry of the scanning and analysis protocol has been performed manually. This involves significant operator time and, further, is a source of errors in the scanning and analysis procedure.